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How do I build a maximum parsimony tree? (Read 3390 times)
Aug 17th, 2019 at 8:00pm

morecoffee   Offline
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Hello all,
I am a student, so bear with me if I'm doing this wrong.

I have aligned some sequences and am looking to do a maximum parsimony tree, for example doing a branch & bound, but I can't find out how. Is this feature missing? Is there a workaround?

Also, I should try to remove uninformative characters before doing so, but can't find a way.

Any help?

Thanks!
 
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Reply #1 - Aug 19th, 2019 at 12:19pm

Olga Golosova   Offline
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Hello,

Quote:
am looking to do a maximum parsimony tree

Unfortunately, this method is not yet integrated into UGENE.

If you'd like to build a tree using another method, see this page: https://ugene.net/wiki/display/UUOUM32/Building+Phylogenetic+Tree.

Quote:
I should try to remove uninformative characters before doing so, but can't find a way.

If you need to remove a region in an alignment, just select the region and click Delete on the keyboard. For other options of editing an alignment, see https://ugene.net/wiki/display/UUOUM32/Editing+Alignment.
 
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Reply #2 - Aug 20th, 2019 at 1:58am

morecoffee   Offline
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Thanks. Should I open a feature request? I am not a programmer, but my guess is that it would take the external tools plugin and use it with something like Nona
 
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Reply #3 - Aug 20th, 2019 at 12:08pm

Olga Golosova   Offline
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Quote:
Should I open a feature request?

We've already taken your feedback into account, however, you might create an issue in our issues tracking system, it's open for everyone.

Let me inform you that unfortunately the issue probably won't be implemented in the nearest UGENE versions in terms of free support. But the more feedbacks like this we have, the earlier the feature is going to be added into UGENE. So, thank you for the feedback anyway!
 
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Reply #4 - Aug 21st, 2019 at 3:08pm

morecoffee   Offline
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Thanks for your quick and kind reply, I opened an Issue as a feature request for it.

i really like Ugene, keep it up!
 
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Reply #5 - Aug 21st, 2019 at 3:11pm

Olga Golosova   Offline
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Quote:
Thanks for your quick and kind reply, I opened an Issue as a feature request for it.

Yes, I see. Thanks!

Quote:
i really like Ugene, keep it up!

We'll do our best!  Smiley
 
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